We have both a '11 335is with DCT and an '11.5 M3 sedan with MT. I had an '08 M3 convertible with DCT for a month that I bought as a CPO, but I found out it had been in an accident and the dealer took it back due to non-disclosure.
Here in PA, we have many back country roads, hills and mountain roads for some fun driving.
I bought the 335is vert after the M3 because the lower end torque in the M3 with DCT struggled to climb the mountain road that we live on, and others like it without having the M Drive engaged. The 335is has much more usuable lower end torque.
The 335is feels more nimble and lighter to me when driving curvy roads and going through tight corners, plus the power band is right there for recovery through the turns. The M3 convertible was heavier in the front end and felt like it was plowing in tight corners.
The 335is has a great sounding exhaust. The M3's engine roar sounds excellent.
Comparing my 335is convertible with DCT to our M3 sedan with MT.
The MT takes care of most of the lower end torque difficiencies that I felt with the M3 with DCT (unless you always use the paddle shifters to drive normally in the M3 which would use more fuel).
The DCT in the 335is is fun. In the sport mode, it rev matches on downshifts and you get the burble and back fires on decel. Also in sport mode automatic, it nearly always picks the right gear depending on your driving circumstance.
The M3 sedan looks more masculine than the coupe or convertible, IMO. The flaired wheel wells and the hood scoop, the front fender side vents and the rear end mufflers and exhaust pipes. It's just a better looking car.
The M3 handles curves noticeably better than the 335is. Minimal body roll (compared to my 911 that has virtually none) and you always feel in control. I sometimes feel like the 335is is going to give away through curves.
The M3 sedan does not feel like it's plowing as much through the corners. I think the extra weight of the convertible hurt the handling of the M3.
During normal driving, the suspension on the M3 with the 3+ selections and the non run-flat tires is a much better setup. It can handle roads like a great daily driver or turn into a track monster. The 335is suspension is very good however, even with my 19" wheels and ultra low profile run flat tires. There are few times when the car feels rough, and the set-up feels kinda like the normal setting in the M3. The selectable M3 suspension just gives you more flexibility.
The M3 as a daily driver is excellent with the M Drive and selectable suspension. You can set it to normal and it is very tame. Set it to sport and it's just plain out fun. The super sport setting is pretty much for the track, IMO. It's just too aggressive for normal spirited street driving.
Both cars are very stable on the highway. There is no bump steer from either at normal settings.
The gas mileage on both is not great. I get an average of 17.5 in FL (I was averaging 14.2 in PA) and my son for normal work commuting in VA is actually getting over 18 MPG.
The cost for maintenenace for the M3 will be much more than the 335is. BMW feels this way too. The Platinum extended warranty for the 335is convertible was (from memory) about $2,800 and the M3 is about $4,800. I'll have to pull out my records for the actual numbers. But, items like brakes and etc. the dealer told me about double the cost to repair the M3 over the 335is.
At the time, I had a ZO6 and was looking for a spirited convertible to also drive for fun. I had first bought the used M3 which was actually less than I paid for my 335is, but I didn't want to pay about $80,000 for the new M3 convertible with similar options to my new 335is which was in the mid $60,000 range. There were not many deals around in the spring of '11 for either car.
If the car is your only car and you save money for maintenance down the road, then I would personally go with the M3 because it is so versatile and it is a really great car.
I am happy with the 335is and will keep it for many years. My wife also loves it and that's primarily why I got one with the DCT. If it was my only sports car, then I would have gone with the M3.
I have not had, nor have I heard of any problems with the HPFP on a 335is.
Let me know if I can answer any other questions because I'm sure there are items I forgot to list.